In the last years of the Forerunner empire, chaos rules. The Flood — a horrifying shape-changing parasite — has arrived in force, aided by unexpected allies. Internal strife within the ecumene has desperately weakened Forerunner defenses. Too little, too late, the legal rate of Juridicals is only now investigating possible crimes by the Master Builder and others. Evidence-gathering agents known collectively as Catalog have been dispatched to collect testimony from the Librarian and both Didacts: the Ur-Didact, treacherously abandoned in a Flood-infested system, and the Bornstellar Didact, who accompanies the Librarian as she preserves specimens against the dire possibility of Halo extermination.

Facing the imminent collapse of their civilization, the Librarian and the Ur-Didact reveal what they know about the relationship between the long-vanished Precursors and the Flood. The Precursors created many technological species, including humanity and the Forerunners. But the roots of the Flood may be found in an act of enormous barbarity, carried out beyond our galaxy ten million years before... Because of that barbarism, a greater evil looms. Only the Ur-Didact and the Librarian -- husband and wife pushed into desperate conflict -- hold the keys to a solution. Facing the consequences of a mythic tragedy, one of them must now commit the greatest atrocity of all time — to prevent an insane evil from dominating the entire universe."[2]

Like the first two novels in the Forerunner Saga, Silentium is framed with an in-universe conceit, being presented as a series of Forerunner logs under investigation by ONI in the modern era. The files in question are said to have been extracted from two sources: the carapace of a deceased Catalog (designated Forerunner remains #879) and a damaged monitor. Both the "Bornstellar Relation", the fictional document that encompasses the narrative of Halo: Cryptum and ONI's recovery of 343 Guilty Spark which acts as the framing device for the plot of Halo: Primordium, are referenced.

In the opening chapter, a Senior Juridical sent under the orders of the Master Juridical meets Haruspis, the guardian of the Domain. He demands to be granted access to classified information pertaining to the Precursors and crimes against the Mantle, but Haruspis refuses him, telling that no one has such authority. Just as the Juridical tells Haruspis that he does have the authority to bypass him, the Domain itself requests to testify to the Juridical, who initially denies that it is even a conscious entity. The Domain then opens itself to the Juridical, who is quickly overwhelmed by the resulting influx of knowledge.

On Erde-Tyrene, Catalog observes the evacuation effort of the planet. Catalog is here to investigate the Battle of the Capital, which resulted in the deaths of the entire Old Council, and demands a testimony from both the Librarian and her husband - the IsoDidact, formerly Bornstellar Makes Eternal Lasting. However, a warning of an approaching Flood fleet results in the IsoDidact having to leave to defend the territory, so Catalog is sent off with the Librarian. While it accompanies her, she tells it about the events that led to her becoming a Lifeshaper, and her growing split from the original Didact due to their differing opinions about humanity.

Over a thousand years earlier, shortly before the Ur-Didact went into exile, he and the Librarian gathered together at their estate on the world of Nomdagro. An associate of Haruspis visited their home and helped guide the Ur-Didact in the Cryptum's preservation process. After the Didact's exile, things continued to deteriorate on the Forerunner political scene. To remain seen as an asset to the Master Builder, the Librarian proposed an expedition to a local galaxy known as Path Kethona to learn about the Flood's origins. Legend dictated that 10 million years ago, ancient Forerunners journeyed to Path Kethona, but actual records detailing this journey had long since vanished. The Old Council approved of this venture and the ship Audacity was constructed for the long journey to Path Kethona. The crew consisted of the Librarian, a Builder named Keeper-of-Tools, a Miner named Clearance-of-Old-Forests, and two Lifeworkers named Chant-to-Green and Birth-to-Light. Arriving at Path Kethona, the crew of Audacity would find it seemingly completely devoid of life. However, they discovered that Precursor architecture existed this far out of the Milky Way. Amongst the artifacts was a vast fleet of ancient Forerunner vessels of war. The Librarian and her crew scanned the Forerunner vessels and found nothing of true interest; any records inside had been destroyed thousands of years ago, as they were uploaded in binary.

Eventually, the Librarian, Keeper and Chant discovered a planet with a civilization of primitive Forerunners confined to the planet and lacking any form of advanced technology; however, the planet's ecology was completely based upon Forerunner genetics. The crew landed on the planet to encounter the natives in person. An old female named Glow-of-Old-Suns took the Librarian to a valley where microbiological growths recorded the locals' history - essentially an organic analog to the Domain. By accessing this information reserve, the Librarian would learn that Warriors drove the Precursors to Path Kethona during the Forerunners' genocidal campaign against their creators ten million years earlier, and that the planet's inhabitants were descendants of Forerunners exiled there as punishment for refusing to partake in the destruction of the Precursors.

Back in the present, the Ur-Didact emerges from a stasis bubble on a broken-down Builder hulk drifting in a Burn (a Flood-infected star system). Also on-board is a former Promethean named Sharp-by-Striking, another Catalog and a Builder named Maker-of-Moons. Sharp lost favor with Faber and Maker was going to give Catalog testimony against Faber, so all three found themselves on the broken ship as well. Their destination is a Flood-infested world called Uthera Midgeerrd. Eventually a Precursor artifact composed of slithering star roads appears and threatens to destroy the ship. The Ur-Didact, willing to confront whatever lies in the Precursor artifact, remains on the ship while the others escape; only Catalog stays to accompany him.

The Ur-Didact and Catalog are captured by the Gravemind and the Ur-Didact's sanity is severely shaken by the resulting encounter. The Gravemind then reveals the true nature of the Precursors. They did indeed reject Forerunners for the Mantle and intended for humans to hold it. The Forerunners did not accept this and drove the Precursors from the galaxy and beyond. Some Precursors survived by going dormant, others became powder that could regenerate their old selves in time, but time rendered it defective and it only created sickness and disease. The Precursors vowed that none of their creations would rise against them again and that all life would suffer and be in perpetual agony, through their new form as the Flood.

Back in the Orion complex, Forerunner defenses continue to fall as the Flood begins to reactivate formerly dormant Precursor artifacts across the galaxy and use them to overwhelm Forerunner fleets. The Master Builder is revealed to be alive and well. He rescued the Ur-Didact, who was given power once again. A meeting occurs on Nomdagro between the IsoDidact, Ur-Didact and Librarian that does not go well. Arguments ensue and the Ur-Didact reveals the Gravemind drove him mad and that he would not let humans attain the Mantle. The Flood arrives and ravages Nomdagro as the Audacity and Mantle's Approach leave towards the greater Ark, now the last bastion of the ecumene.

On the greater Ark, Omega Halo is there in anticipation for a Flood assault. A power struggle ensues between the IsoDidact and other Forerunner commanders who think the Ur-Didact should instead lead them. The Master Builder manages to regain control for him and the IsoDidact by revealing that the Ur-Didact is being used as a pawn for the Gravemind; after Faber had recovered him, the Ur-Didact conveyed him a sadistic message from the Gravemind which had absorbed Faber's family.

A massive Flood fleet led by Mendicant Bias arrives and chaos erupts. In that confusion, the Ur-Didact uses a Composer to compose human populations being stored on Omega Halo and retreats towards Requiem. The Librarian follows behind him, grieving for the loss of her humans. Monitor Chakas is tasked with saving the rest of the humans on the Ark and taking them to the lesser Ark, still hidden from the Ur-Didact and the Flood. The IsoDidact and the remaining Forerunner commanders with Faber in tow go to the Halo and activate it to buy time. Although the pulse destroys some of the Precursor star roads and part of the Flood fleet, both the greater Ark and Omega Halo are soon destroyed by the star roads. Faber remains behind while IsoDidact and the other commanders attempt to escape, but they begin to plummet to their deaths as the Halo is torn apart. Chakas manages to save the IsoDidact and takes him to the lesser Ark via Faber's personal slipspace portal.

On Requiem, the Librarian sneaks aboard with the Audacity by trailing behind the Mantle's Approach. Requiem's defenses also view her as a friendly and let her in. The Librarian finds Endurance-of-Will, a Promethean and former lover of the Ur-Didact. Endurance reveals that the Ur-Didact is using the essences of the composed humans and Prometheans to create mechanical Promethean Knights, with which he plans to defeat the Flood and eradicate all species who might challenge the Forerunners in the future. Despite resenting her for being chosen by the Ur-Didact instead of her, Endurance is eventually convinced to help the Librarian take down the Ur-Didact and seal him in a Cryptum. Once done, the Librarian tasks Endurance to watch over the Didact for as long as she can. As she leaves Requiem for Earth, the Librarian is confronted by a large group of Knights, which she takes command of, and wonders if Endurance chose to become one herself.

The Librarian then draws the Flood towards Earth to allow the IsoDidact to fire the seven Halo rings. She sends Chant-to-Green off to the lesser Ark with the planet's remaining humans and passes her title of Lifeshaper on to Chant while remaining on Earth herself. During her last days on Earth, the Gravemind sends down ancient human essences, including the Lord of Admirals, to reveal that the Domain was created by the Precursors as the collection of wisdom from over 100 billion years of knowledge and that it was ingrained in Precursor architecture for safekeeping. In short, the Domain is the mythical Organon. Sadly, the Librarian realizes that the Halos will destroy all of this, and that without the Domain, the Ur-Didact will spend the eons to come in complete silence, dwelling on his own madness and rage. As she watches the Portal's construction, she sincerely hopes humanity will one day inherit the Mantle.

At the lesser Ark, the IsoDidact activates the rings while Offensive Biasfends off Mendicant Bias' fleet, allowing the rings to fire before the latter can reach the Ark. In the end, 343 Guilty Spark reflects on the Halos working their power throughout the galaxy. In that instant, he receives the first signals of a young, previously-unknown civilization, which is swiftly extinguished by the Array's pulse. Compartmentalization processes then erase large portions of Spark's memory and he forgets his old life.

A code to a hidden audio epilogue, titled "Rebirth", is included in the form of Forerunner symbols featured in some of the chapter headings for the novel. The code can be used on Halo Waypoint to unlock a forty-minute narration by Greg Bear, describing the reintroduction phase from the perspective of Riser. Having survived the destruction of the greater Ark, Riser, Vinnevra and other humans are relocated on Installation 00 among many other species, where Forerunners watch over them until they are returned to their homeworld. At Riser's request, his people are relocated on a series of islands. Riser meets with the IsoDidact one last time before the Forerunners leave and the humans begin settling in their new home. Days after, a new code was revealed, adding 5 additional minutes to the epilogue, describing the trial of Mendicant Bias after its defeat at the Battle of the Maginot Sphere.[3]

The novel was originally set to be released on January 8, 2013,[4] but the release was later delayed to March 19.[1] For the last three months of the novel's writing process, Greg Bear worked closely with 343 Industries Franchise Writer Jeremy Patenaude to incorporate story elements from Halo 4 and other fiction and to ensure that the stories fit together seamlessly.[5][6] A number of additional references to previous continuity were also included to the novel as a result of this collaboration. Greg Bear jokingly noted that he and Patenaude bonded as "blood brothers" and stated that he calls Patenaude "boss".[5]

The preliminary cover art for the novel, illustrated by Nicolas "Sparth" Bouvier, depicts a vast Forerunner structure with a Cryptum floating in the center and several ships flying by, while the final cover art depicts the Ur-Didact observing a hologram of a Cryptum and his wife, the Librarian; the preliminary cover image remains in the background, although the Cryptum in the background is absent. The original cover illustration was used to promote the novel without giving spoilers as to the appearance of the Forerunner characters, which was not revealed until Halo 4. The final cover art was done as a collaboration between Sparth and Halo 4 concept artist Gabriel Garza.[7]

On February 11, 2013, an announcement was released on Halo Waypoint that in the weeks leading up to the release of Silentium Tor Books and 343 Industries would be sending out encrypted communications via halowaypoint.com bulletins and forums, which will allow fans to unlock additional content. There will also be embedded data in the text of the Halo: Silentium paperback and e-book editions.[8] Players can unlock this content in the Classified menu at Halo Waypoint. The unlocked contents are 20,000 experience points for multiplayer and an audio video called "Rebirth", a story narrated by Greg Bear and acts as an epilogue for Silentium. It tells the story of Riser and his last encounter with the IsoDidact. Days after, a new code was revealed, adding 50,000 XP, a new emblem (Overachiever), and 5 additional minutes to Epilogue "Rebirth", which consist of a trial made ​​by the Forerunners survivors to Mendicant Bias after the latter's defeat against Offensive Bias.

Similar to the preceding novels, a sneak peek of the first two chapters of the novel was released on Halo Waypoint and Tor.com on March 13, 2013.[9]

"Silentium" is Latin for "silence", "stillness", "inactivity" or "cessation", which reflects the effect of the Halo Array's galaxy-wide activation on the Forerunner civilization and life in the galaxy. It is also the last word in the novel, appearing as a line spoken by 343 Guilty Spark as the Halo Array fires and he forgets his humanity.[10]

The Ur-Didact exclaims "And loose damnation on the stars?" in retort to the IsoDidact's statement that using the Halos may be the Forerunners' only chance to stop the Flood.[11] This is a reference to a line spoken by Cortana on the level The Covenant in Halo 3: "For a moment of safety, I loosed damnation upon the stars.".

During his final conversation with 343 Guilty Spark, before deploying the Halo Array, the IsoDidact asks the monitor "Tell me, Chakas, if this was your choice, after all we have seen and survived... would you fire the rings?"[12] This references a statement made by Guilty Spark to John-117 in the opening cinematic of the level Two Betrayals in Halo: Combat Evolved: "Last time, you asked me, if it were my choice, would I do it? Having had considerable time to ponder your query, my answer has not changed."

The novel describes a gathering of the Halo installation monitors aboard a Lifeworker vessel over the lesser Ark before the deployment of the Halos. This was first shown in the terminals of Halo: Combat Evolved Anniversary.

The description of the Halo Array being launched from the lesser Ark via a portal closely echoes the depiction of the event from Origins. However, Origins shows all seven of the final Halos entering the portal, whereas in Silentium there are only six, as Installation 07 had been deployed years earlier.[13]

The Didact's pose in the cover art (with his hands closing around his Cryptum) foreshadows the manner in which Precursor star roads destroy planets.